/*
 * Copyright 2014 Davy Maddelein.
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package com.compomics.pepshell.controllers.secondarystructureprediction;

import com.compomics.pepshell.controllers.DAO.PDBDAO;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;

/**
 *
 * @author Davy Maddelein
 */
public class PDBSecondaryStructurePredictor extends SecondaryStructurePrediction {

    @Override
    public List<String> getPrediction(String pdbAccession) throws IOException {
        List<String> secondaryStructure = new ArrayList<>();
        String pdbFile = PDBDAO.getPdbFileInMem(pdbAccession);
        String[] pdbLines = pdbFile.split("\n");
        for (String aPdbLine : pdbLines) {
            if (aPdbLine.startsWith("HELIX")) {
                aPdbLine.split(" ");
            }
            if (aPdbLine.startsWith("SHEET")) {
                aPdbLine.split(" ");
            }
        }
        return secondaryStructure;
    }

}
